Flooding events in coastal bodies of water have remarkable influence on fish habitats resulting in the alterations in distribution and abundance of some fish populations. As a first step in the evaluation of the effects of flooding events in the Gulf coast, Penn State/NCAR Mesoscale model (MM5) simulations were used to forecast and seek a better understanding of the physics associated with the 1995 flood event. The model was run on doubly nested domain centered over the Mississippi Sound of the Gulf of Mexico, with a grid spacing of 90 km and 30 km. MM5 was run for 6hour periods, from the initial period of storm development, 8th May through the 10th of May, and during non-flood period of 1996. Model simulations of sea surface temperatures, salinities and river discharge will be related to abundance data in the Mississippi Sound to assess the influence of flooding on fish populations.